Correlation between gene mutation status and molecular subtypes

Overview

Introduction

This pipeline computes the correlation between significantly recurrent gene mutations and molecular subtypes.

Summary

Testing the association between mutation status of 8 genes and 10 molecular subtypes across 179 patients, 24 significant findings detected with P value < 0.05 and Q value < 0.25.

HRAS mutation correlated to 'CN_CNMF', 'METHLYATION_CNMF', 'RPPA_CHIERARCHICAL', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
NF1 mutation correlated to 'METHLYATION_CNMF', 'RPPA_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.
EPAS1 mutation correlated to 'METHLYATION_CNMF', 'MRNASEQ_CNMF', 'MRNASEQ_CHIERARCHICAL', 'MIRSEQ_CNMF', 'MIRSEQ_CHIERARCHICAL', 'MIRSEQ_MATURE_CNMF', and 'MIRSEQ_MATURE_CHIERARCHICAL'.

Results

Overview of the results

Table 1. Get Full Table Overview of the association between mutation status of 8 genes and 10 molecular subtypes. Shown in the table are P values (Q values). Thresholded by P value < 0.05 and Q value < 0.25, 24 significant findings detected.


		Clinical Features	CN CNMF	METHLYATION CNMF	RPPA CNMF	RPPA CHIERARCHICAL	MRNASEQ CNMF	MRNASEQ CHIERARCHICAL	MIRSEQ CNMF	MIRSEQ CHIERARCHICAL	MIRSEQ MATURE CNMF	MIRSEQ MATURE CHIERARCHICAL
	nMutated (%)	nWild-Type	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test	Fisher's exact test
HRAS	18 (10%)	161	8e-05 (0.000914)	7e-05 (0.000914)	0.155 (0.401)	0.00133 (0.00811)	1e-05 (0.000267)	1e-05 (0.000267)	1e-05 (0.000267)	0.00024 (0.00213)	0.00052 (0.00416)	5e-05 (0.000914)
NF1	15 (8%)	164	0.574 (0.883)	0.00564 (0.0237)	0.00717 (0.0287)	0.0884 (0.253)	0.00974 (0.0354)	0.00012 (0.0012)	0.00071 (0.00516)	0.00553 (0.0237)	0.0176 (0.0613)	0.00965 (0.0354)
EPAS1	8 (4%)	171	0.181 (0.453)	0.00323 (0.0152)	0.354 (0.712)	0.356 (0.712)	0.00203 (0.0108)	0.00142 (0.00811)	0.00096 (0.0064)	0.0189 (0.063)	0.00298 (0.0149)	6e-05 (0.000914)
NUDT11	5 (3%)	174	0.907 (1.00)	0.719 (0.975)	0.788 (1.00)	1 (1.00)	0.341 (0.712)	0.675 (0.965)	0.37 (0.721)	0.281 (0.643)	0.836 (1.00)	0.694 (0.97)
RET	6 (3%)	173	0.434 (0.79)	0.424 (0.79)	0.429 (0.79)	0.324 (0.701)	0.0873 (0.253)	0.0982 (0.271)	0.507 (0.845)	0.062 (0.198)	0.249 (0.587)	0.468 (0.796)
SHROOM4	3 (2%)	176		1 (1.00)			0.462 (0.796)	0.543 (0.876)	1 (1.00)	0.676 (0.965)	0.916 (1.00)	0.859 (1.00)
AMMECR1	3 (2%)	176	0.458 (0.796)	1 (1.00)	0.548 (0.876)	1 (1.00)	0.241 (0.583)	0.627 (0.929)	0.79 (1.00)	1 (1.00)	0.605 (0.913)	0.143 (0.381)
GPR128	4 (2%)	175	0.563 (0.883)	0.0758 (0.233)			0.889 (1.00)	0.887 (1.00)	0.295 (0.655)	0.879 (1.00)	0.703 (0.97)	0.979 (1.00)

'HRAS MUTATION STATUS' versus 'CN_CNMF'

P value = 8e-05 (Fisher's exact test), Q value = 0.00091

Table S1. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
HRAS MUTATED	1	0	5	7	2
HRAS WILD-TYPE	36	40	5	43	23

Figure S1. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

'HRAS MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 7e-05 (Fisher's exact test), Q value = 0.00091

Table S2. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
HRAS MUTATED	0	17	1
HRAS WILD-TYPE	45	67	49

Figure S2. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'HRAS MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.155 (Fisher's exact test), Q value = 0.4

Table S3. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
HRAS MUTATED	3	2	5	0
HRAS WILD-TYPE	14	19	18	18

'HRAS MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.00133 (Fisher's exact test), Q value = 0.0081

Table S4. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
HRAS MUTATED	1	7	2
HRAS WILD-TYPE	32	11	26

Figure S3. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S5. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
HRAS MUTATED	0	18	0	0
HRAS WILD-TYPE	38	52	50	21

Figure S4. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S6. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
HRAS MUTATED	0	18	0	0
HRAS WILD-TYPE	39	53	48	21

Figure S5. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1e-05 (Fisher's exact test), Q value = 0.00027

Table S7. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
HRAS MUTATED	0	2	16
HRAS WILD-TYPE	72	42	47

Figure S6. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00024 (Fisher's exact test), Q value = 0.0021

Table S8. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
HRAS MUTATED	1	14	1	2
HRAS WILD-TYPE	76	45	17	23

Figure S7. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00052 (Fisher's exact test), Q value = 0.0042

Table S9. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
HRAS MUTATED	1	12	4	1	0
HRAS WILD-TYPE	34	44	13	39	30

Figure S8. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'HRAS MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 5e-05 (Fisher's exact test), Q value = 0.00091

Table S10. Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
HRAS MUTATED	0	9	0	7	0	1	1
HRAS WILD-TYPE	21	38	31	9	26	17	18

Figure S9. Get High-res Image Gene #1: 'HRAS MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.574 (Fisher's exact test), Q value = 0.88

Table S11. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
NF1 MUTATED	2	3	1	7	1
NF1 WILD-TYPE	35	37	9	43	24

'NF1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00564 (Fisher's exact test), Q value = 0.024

Table S12. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
NF1 MUTATED	1	13	1
NF1 WILD-TYPE	44	71	49

Figure S10. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.00717 (Fisher's exact test), Q value = 0.029

Table S13. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
NF1 MUTATED	3	0	6	0
NF1 WILD-TYPE	14	21	17	18

Figure S11. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

'NF1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.0884 (Fisher's exact test), Q value = 0.25

Table S14. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
NF1 MUTATED	1	4	4
NF1 WILD-TYPE	32	14	24

'NF1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00974 (Fisher's exact test), Q value = 0.035

Table S15. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
NF1 MUTATED	3	11	0	1
NF1 WILD-TYPE	35	59	50	20

Figure S12. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00012 (Fisher's exact test), Q value = 0.0012

Table S16. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
NF1 MUTATED	0	14	0	1
NF1 WILD-TYPE	39	57	48	20

Figure S13. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00071 (Fisher's exact test), Q value = 0.0052

Table S17. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
NF1 MUTATED	1	2	12
NF1 WILD-TYPE	71	42	51

Figure S14. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.00553 (Fisher's exact test), Q value = 0.024

Table S18. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
NF1 MUTATED	2	11	0	2
NF1 WILD-TYPE	75	48	18	23

Figure S15. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.0176 (Fisher's exact test), Q value = 0.061

Table S19. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
NF1 MUTATED	2	10	2	1	0
NF1 WILD-TYPE	33	46	15	39	30

Figure S16. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'NF1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.00965 (Fisher's exact test), Q value = 0.035

Table S20. Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
NF1 MUTATED	3	9	0	2	0	0	1
NF1 WILD-TYPE	18	38	31	14	26	18	18

Figure S17. Get High-res Image Gene #2: 'NF1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.181 (Fisher's exact test), Q value = 0.45

Table S21. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
EPAS1 MUTATED	2	5	0	1	0
EPAS1 WILD-TYPE	35	35	10	49	25

'EPAS1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.00323 (Fisher's exact test), Q value = 0.015

Table S22. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
EPAS1 MUTATED	5	0	3
EPAS1 WILD-TYPE	40	84	47

Figure S18. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

'EPAS1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.354 (Fisher's exact test), Q value = 0.71

Table S23. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
EPAS1 MUTATED	1	3	1	0
EPAS1 WILD-TYPE	16	18	22	18

'EPAS1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.356 (Fisher's exact test), Q value = 0.71

Table S24. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
EPAS1 MUTATED	2	0	3
EPAS1 WILD-TYPE	31	18	25

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.00203 (Fisher's exact test), Q value = 0.011

Table S25. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
EPAS1 MUTATED	1	0	7	0
EPAS1 WILD-TYPE	37	70	43	21

Figure S19. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.00142 (Fisher's exact test), Q value = 0.0081

Table S26. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
EPAS1 MUTATED	1	0	7	0
EPAS1 WILD-TYPE	38	71	41	21

Figure S20. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.00096 (Fisher's exact test), Q value = 0.0064

Table S27. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
EPAS1 MUTATED	8	0	0
EPAS1 WILD-TYPE	64	44	63

Figure S21. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.0189 (Fisher's exact test), Q value = 0.063

Table S28. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
EPAS1 MUTATED	8	0	0	0
EPAS1 WILD-TYPE	69	59	18	25

Figure S22. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.00298 (Fisher's exact test), Q value = 0.015

Table S29. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
EPAS1 MUTATED	0	0	1	6	1
EPAS1 WILD-TYPE	35	56	16	34	29

Figure S23. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

'EPAS1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 6e-05 (Fisher's exact test), Q value = 0.00091

Table S30. Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
EPAS1 MUTATED	1	0	0	0	7	0	0
EPAS1 WILD-TYPE	20	47	31	16	19	18	19

Figure S24. Get High-res Image Gene #3: 'EPAS1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

'NUDT11 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.907 (Fisher's exact test), Q value = 1

Table S31. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
NUDT11 MUTATED	1	2	0	2	0
NUDT11 WILD-TYPE	36	38	10	48	25

'NUDT11 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.719 (Fisher's exact test), Q value = 0.97

Table S32. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
NUDT11 MUTATED	2	2	1
NUDT11 WILD-TYPE	43	82	49

'NUDT11 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.788 (Fisher's exact test), Q value = 1

Table S33. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
NUDT11 MUTATED	1	0	1	1
NUDT11 WILD-TYPE	16	21	22	17

'NUDT11 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S34. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
NUDT11 MUTATED	1	1	1
NUDT11 WILD-TYPE	32	17	27

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.341 (Fisher's exact test), Q value = 0.71

Table S35. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
NUDT11 MUTATED	2	3	0	0
NUDT11 WILD-TYPE	36	67	50	21

'NUDT11 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.675 (Fisher's exact test), Q value = 0.97

Table S36. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
NUDT11 MUTATED	0	3	2	0
NUDT11 WILD-TYPE	39	68	46	21

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.37 (Fisher's exact test), Q value = 0.72

Table S37. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
NUDT11 MUTATED	2	0	3
NUDT11 WILD-TYPE	70	44	60

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.281 (Fisher's exact test), Q value = 0.64

Table S38. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
NUDT11 MUTATED	1	4	0	0
NUDT11 WILD-TYPE	76	55	18	25

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.836 (Fisher's exact test), Q value = 1

Table S39. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
NUDT11 MUTATED	1	3	0	1	0
NUDT11 WILD-TYPE	34	53	17	39	30

'NUDT11 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.694 (Fisher's exact test), Q value = 0.97

Table S40. Gene #4: 'NUDT11 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
NUDT11 MUTATED	1	3	0	0	1	0	0
NUDT11 WILD-TYPE	20	44	31	16	25	18	19

'RET MUTATION STATUS' versus 'CN_CNMF'

P value = 0.434 (Fisher's exact test), Q value = 0.79

Table S41. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
RET MUTATED	3	0	0	2	1
RET WILD-TYPE	34	40	10	48	24

'RET MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.424 (Fisher's exact test), Q value = 0.79

Table S42. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
RET MUTATED	0	4	2
RET WILD-TYPE	45	80	48

'RET MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.429 (Fisher's exact test), Q value = 0.79

Table S43. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
RET MUTATED	1	0	2	0
RET WILD-TYPE	16	21	21	18

'RET MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 0.324 (Fisher's exact test), Q value = 0.7

Table S44. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
RET MUTATED	0	1	2
RET WILD-TYPE	33	17	26

'RET MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.0873 (Fisher's exact test), Q value = 0.25

Table S45. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
RET MUTATED	0	5	0	1
RET WILD-TYPE	38	65	50	20

'RET MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.0982 (Fisher's exact test), Q value = 0.27

Table S46. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
RET MUTATED	0	5	0	1
RET WILD-TYPE	39	66	48	20

'RET MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.507 (Fisher's exact test), Q value = 0.84

Table S47. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
RET MUTATED	1	2	3
RET WILD-TYPE	71	42	60

'RET MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.062 (Fisher's exact test), Q value = 0.2

Table S48. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
RET MUTATED	0	4	1	1
RET WILD-TYPE	77	55	17	24

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.249 (Fisher's exact test), Q value = 0.59

Table S49. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
RET MUTATED	1	4	1	0	0
RET WILD-TYPE	34	52	16	40	30

'RET MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.468 (Fisher's exact test), Q value = 0.8

Table S50. Gene #5: 'RET MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
RET MUTATED	0	3	0	1	0	1	1
RET WILD-TYPE	21	44	31	15	26	17	18

'SHROOM4 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S51. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
SHROOM4 MUTATED	1	1	1
SHROOM4 WILD-TYPE	44	83	49

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.462 (Fisher's exact test), Q value = 0.8

Table S52. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
SHROOM4 MUTATED	1	1	0	1
SHROOM4 WILD-TYPE	37	69	50	20

'SHROOM4 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.543 (Fisher's exact test), Q value = 0.88

Table S53. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
SHROOM4 MUTATED	0	1	1	1
SHROOM4 WILD-TYPE	39	70	47	20

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S54. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
SHROOM4 MUTATED	1	1	1
SHROOM4 WILD-TYPE	71	43	62

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.676 (Fisher's exact test), Q value = 0.97

Table S55. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
SHROOM4 MUTATED	1	1	0	1
SHROOM4 WILD-TYPE	76	58	18	24

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.916 (Fisher's exact test), Q value = 1

Table S56. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
SHROOM4 MUTATED	0	1	0	1	1
SHROOM4 WILD-TYPE	35	55	17	39	29

'SHROOM4 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.859 (Fisher's exact test), Q value = 1

Table S57. Gene #6: 'SHROOM4 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
SHROOM4 MUTATED	0	1	1	0	0	0	1
SHROOM4 WILD-TYPE	21	46	30	16	26	18	18

'AMMECR1 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.458 (Fisher's exact test), Q value = 0.8

Table S58. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
AMMECR1 MUTATED	0	0	0	2	1
AMMECR1 WILD-TYPE	37	40	10	48	24

'AMMECR1 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 1 (Fisher's exact test), Q value = 1

Table S59. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
AMMECR1 MUTATED	1	1	1
AMMECR1 WILD-TYPE	44	83	49

'AMMECR1 MUTATION STATUS' versus 'RPPA_CNMF'

P value = 0.548 (Fisher's exact test), Q value = 0.88

Table S60. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #3: 'RPPA_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	17	21	23	18
AMMECR1 MUTATED	0	2	1	0
AMMECR1 WILD-TYPE	17	19	22	18

'AMMECR1 MUTATION STATUS' versus 'RPPA_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S61. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #4: 'RPPA_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	33	18	28
AMMECR1 MUTATED	1	1	1
AMMECR1 WILD-TYPE	32	17	27

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.241 (Fisher's exact test), Q value = 0.58

Table S62. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
AMMECR1 MUTATED	1	0	2	0
AMMECR1 WILD-TYPE	37	70	48	21

'AMMECR1 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.627 (Fisher's exact test), Q value = 0.93

Table S63. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
AMMECR1 MUTATED	0	1	2	0
AMMECR1 WILD-TYPE	39	70	46	21

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.79 (Fisher's exact test), Q value = 1

Table S64. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
AMMECR1 MUTATED	2	0	1
AMMECR1 WILD-TYPE	70	44	62

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 1 (Fisher's exact test), Q value = 1

Table S65. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
AMMECR1 MUTATED	2	1	0	0
AMMECR1 WILD-TYPE	75	58	18	25

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.605 (Fisher's exact test), Q value = 0.91

Table S66. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
AMMECR1 MUTATED	0	1	0	2	0
AMMECR1 WILD-TYPE	35	55	17	38	30

'AMMECR1 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.143 (Fisher's exact test), Q value = 0.38

Table S67. Gene #7: 'AMMECR1 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
AMMECR1 MUTATED	1	0	0	0	2	0	0
AMMECR1 WILD-TYPE	20	47	31	16	24	18	19

'GPR128 MUTATION STATUS' versus 'CN_CNMF'

P value = 0.563 (Fisher's exact test), Q value = 0.88

Table S68. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #1: 'CN_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	37	40	10	50	25
GPR128 MUTATED	1	1	0	0	1
GPR128 WILD-TYPE	36	39	10	50	24

'GPR128 MUTATION STATUS' versus 'METHLYATION_CNMF'

P value = 0.0758 (Fisher's exact test), Q value = 0.23

Table S69. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #2: 'METHLYATION_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	45	84	50
GPR128 MUTATED	3	1	0
GPR128 WILD-TYPE	42	83	50

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CNMF'

P value = 0.889 (Fisher's exact test), Q value = 1

Table S70. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #5: 'MRNASEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	38	70	50	21
GPR128 MUTATED	1	1	2	0
GPR128 WILD-TYPE	37	69	48	21

'GPR128 MUTATION STATUS' versus 'MRNASEQ_CHIERARCHICAL'

P value = 0.887 (Fisher's exact test), Q value = 1

Table S71. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #6: 'MRNASEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	39	71	48	21
GPR128 MUTATED	1	1	2	0
GPR128 WILD-TYPE	38	70	46	21

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CNMF'

P value = 0.295 (Fisher's exact test), Q value = 0.66

Table S72. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #7: 'MIRSEQ_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3
ALL	72	44	63
GPR128 MUTATED	3	1	0
GPR128 WILD-TYPE	69	43	63

'GPR128 MUTATION STATUS' versus 'MIRSEQ_CHIERARCHICAL'

P value = 0.879 (Fisher's exact test), Q value = 1

Table S73. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #8: 'MIRSEQ_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4
ALL	77	59	18	25
GPR128 MUTATED	3	1	0	0
GPR128 WILD-TYPE	74	58	18	25

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CNMF'

P value = 0.703 (Fisher's exact test), Q value = 0.97

Table S74. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #9: 'MIRSEQ_MATURE_CNMF'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5
ALL	35	56	17	40	30
GPR128 MUTATED	0	1	0	2	1
GPR128 WILD-TYPE	35	55	17	38	29

'GPR128 MUTATION STATUS' versus 'MIRSEQ_MATURE_CHIERARCHICAL'

P value = 0.979 (Fisher's exact test), Q value = 1

Table S75. Gene #8: 'GPR128 MUTATION STATUS' versus Molecular Subtype #10: 'MIRSEQ_MATURE_CHIERARCHICAL'

nPatients	CLUS_1	CLUS_2	CLUS_3	CLUS_4	CLUS_5	CLUS_6	CLUS_7
ALL	21	47	31	16	26	18	19
GPR128 MUTATED	1	1	1	0	1	0	0
GPR128 WILD-TYPE	20	46	30	16	25	18	19

Methods & Data

Input

Mutation data file = sample_sig_gene_table.txt from Mutsig_2CV pipeline
Processed Mutation data file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/22569696/transformed.cor.cli.txt
Molecular subtypes file = /xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/PCPG-TP/22542422/PCPG-TP.transferedmergedcluster.txt
Number of patients = 179
Number of significantly mutated genes = 8
Number of Molecular subtypes = 10
Exclude genes that fewer than K tumors have mutations, K = 3

Fisher's exact test

For binary or multi-class clinical features (nominal or ordinal), two-tailed Fisher's exact tests (Fisher 1922) were used to estimate the P values using the 'fisher.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

References

[1] Fisher, R.A., On the interpretation of chi-square from contingency tables, and the calculation of P, Journal of the Royal Statistical Society 85(1):87-94 (1922)

[2] Benjamini and Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the Royal Statistical Society Series B 59:289-300 (1995)

Made with Nozzle